.mailmap

@@ -72,3 +72,9 @@ Zhang Ning <zhangning737@gmail.com> Rooney <43574869+zhangning737@users.noreply.
 Zhang Ning <zhangning737@gmail.com> zhangning737 <zhangning737@gmail.com>
 dependabot[bot] <no-email> dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 dependabot[bot] <no-email> dependabot[bot] <dependabot[bot]@users.noreply.github.com>
+Robert Habel <Robert.Habel@student.tu-freiberg.de> Robert Habel <robert.habel@student.tu-freiberg.de>
+Linda Günther <linda.guenther@student.tu-freiberg.de> Linda Günther <Linda.Guenther@student.tu-freiberg.de>
+Sophia Einspänner <sophia.einspaenner@student.tu-freiberg.de> Sophia Einspänner <Sophia.Einspaenner@student.tu-freiberg.de>
+Jakob Randow <jakob.randow@web.de> jrandow <jakob.randow@htwk-leipzig.de>
+Jakob Randow <jakob.randow@web.de> jrandow <jakob.randow@web.de>
+Olaf Kolditz <olaf.kolditz@ufz.de>

.vale.ini

@@ -10,9 +10,9 @@ Packages = Hugo
 BasedOnStyles = Vale, write-good, ogs
 Vale.Spelling = None
 write-good.ThereIs = suggestion
-write-good.Passive = suggestion
-write-good.TooWordy = suggestion
-write-good.Weasel = suggestion
+write-good.Passive = None
+write-good.TooWordy = None
+write-good.Weasel = None
 write-good.E-Prime = None
 
 TokenIgnores = \

CITATION.cff

@@ -10,8 +10,11 @@ license: BSD-3-Clause
 doi: 10.5281/zenodo.591265
 # The following needs to be adapted on releases:
 version: "6.4.3"
-date-released: "2022-04-01"
+date-released: "2022-09-19"
 identifiers:
+    - type: doi
+      description: "Zenodo DOI for 6.4.3"
+      value: 10.5281/zenodo.7092676
     - type: doi
       description: "Zenodo DOI for 6.4.2"
       value: 10.5281/zenodo.6405711

ProcessLib/HydroMechanics/Tests.cmake

@@ -277,7 +277,7 @@ AddTest(
     REQUIREMENTS NOT OGS_USE_MPI
     DIFF_DATA
     expected_square_1e2_UC_late_ts_10_t_1000.000000.vtu square_1e2_UC_late_ts_10_t_1000.000000.vtu displacement displacement 1e-13 1e-16
-    expected_square_1e2_UC_late_ts_10_t_1000.000000.vtu square_1e2_UC_late_ts_10_t_1000.000000.vtu pressure pressure 1e-13 1e-16
+    expected_square_1e2_UC_late_ts_10_t_1000.000000.vtu square_1e2_UC_late_ts_10_t_1000.000000.vtu pressure pressure 2e-13 1e-16
 )
 
 AddTest(

ProcessLib/Utils/SetOrGetIntegrationPointData.h

@@ -16,7 +16,7 @@
 
 #include "BaseLib/DynamicSpan.h"
 #include "MathLib/KelvinVector.h"
-#include "MathLib/LinAlg/Eigen/EigenMapTools.h"
+#include "TransposeInPlace.h"
 
 namespace ProcessLib
 {
@@ -65,17 +65,25 @@ std::vector<double> const& getIntegrationPointKelvinVectorData(
     return cache;
 }
 
+//! Overload without \c cache argument.
+//!
+//! \note This function returns the data in transposed storage order compared to
+//! the overloads that have a \c cache argument.
 template <int DisplacementDim, typename IntegrationPointDataVector,
           typename MemberType>
 std::vector<double> getIntegrationPointKelvinVectorData(
     IntegrationPointDataVector const& ip_data_vector, MemberType member)
 {
-    std::vector<double> ip_kelvin_vector_values;
-
-    getIntegrationPointKelvinVectorData<DisplacementDim>(
-        ip_data_vector, member, ip_kelvin_vector_values);
+    constexpr int kelvin_vector_size =
+        MathLib::KelvinVector::kelvin_vector_dimensions(DisplacementDim);
 
-    return ip_kelvin_vector_values;
+    return transposeInPlace<kelvin_vector_size>(
+        [&](std::vector<double>& values)
+        {
+            return getIntegrationPointKelvinVectorData<DisplacementDim>(
+                ip_data_vector, member, values);
+            ;
+        });
 }
 
 template <int DisplacementDim, typename IntegrationPointDataVector,
@@ -207,9 +215,9 @@ std::vector<double> getIntegrationPointDataMaterialStateVariables(
     std::vector<double> result;
     result.reserve(ip_data_vector.size() * n_components);
 
-    for (auto& ip_data_vector : ip_data_vector)
+    for (auto& ip_data : ip_data_vector)
     {
-        auto const values_span = get_values_span(*(ip_data_vector.*member));
+        auto const values_span = get_values_span(*(ip_data.*member));
         assert(values_span.size() == static_cast<std::size_t>(n_components));
 
         result.insert(end(result), values_span.begin(), values_span.end());
@@ -230,7 +238,7 @@ std::size_t setIntegrationPointDataMaterialStateVariables(
     auto const n_integration_points = ip_data_vector.size();
 
     std::size_t position = 0;
-    for (auto& ip_data : ip_data_vector)
+    for (auto const& ip_data : ip_data_vector)
     {
         auto const values_span = get_values_span(*(ip_data.*member));
         std::copy_n(values + position, values_span.size(), values_span.begin());

Tests/Data/Mechanics/MohrCoulombAbboSloan/slope.prj

@@ -41,7 +41,7 @@
                 <convergence_criterion>
                     <type>DeltaX</type>
                     <norm_type>NORM2</norm_type>
-                    <reltol>1e-14</reltol>
+                    <reltol>1e-13</reltol>
                 </convergence_criterion>
                 <time_discretization>
                     <type>BackwardEuler</type>

Tests/ProcessLib/TestIPDataAccess.cpp

+/**
+ * \file
+ * \copyright
+ * Copyright (c) 2012-2022, OpenGeoSys Community (http://www.opengeosys.org)
+ *            Distributed under a Modified BSD License.
+ *              See accompanying file LICENSE.txt or
+ *              http://www.opengeosys.org/project/license
+ */
+
+#include <gmock/gmock-matchers.h>
+#include <gtest/gtest.h>
+
+#include "ProcessLib/Utils/SetOrGetIntegrationPointData.h"
+
+template <int DisplacementDim>
+struct IPData
+{
+    using KV = MathLib::KelvinVector::KelvinVectorType<DisplacementDim>;
+
+    KV kelvin;
+    double scalar;
+};
+
+template <class Dim>
+struct ProcessLib_IPDataAccess : ::testing::Test
+{
+    static constexpr int dim = Dim::value;
+    static constexpr int kv_size =
+        MathLib::KelvinVector::kelvin_vector_dimensions(dim);
+
+    static std::vector<IPData<Dim::value>> getIPData()
+    {
+        using KV = typename IPData<dim>::KV;
+
+        constexpr int off_diag_size = dim == 2 ? 1 : 3;
+
+        constexpr std::size_t num_int_pts = 10;
+
+        std::vector<IPData<dim>> ip_data(num_int_pts);
+
+        for (std::size_t i = 0; i < num_int_pts; ++i)
+        {
+            ip_data[i].kelvin =
+                KV::Constant(10. * i) + KV::LinSpaced(0., kv_size - 1.);
+
+            // compensate Kelvin vector <-> symmetric tensor conversion
+            ip_data[i].kelvin.template tail<off_diag_size>() *= std::sqrt(2.0);
+
+            ip_data[i].scalar = 10. * num_int_pts + i;
+        }
+
+        return ip_data;
+    }
+
+    static std::vector<IPData<Dim::value>> getIPDataNaNs()
+    {
+        using KV = typename IPData<dim>::KV;
+
+        constexpr std::size_t num_int_pts = 10;
+        constexpr double nan = std::numeric_limits<double>::quiet_NaN();
+
+        std::vector<IPData<dim>> ip_data(num_int_pts);
+
+        for (std::size_t i = 0; i < num_int_pts; ++i)
+        {
+            ip_data[i].kelvin = KV::Constant(nan);
+            ip_data[i].scalar = nan;
+        }
+
+        return ip_data;
+    }
+
+    static std::vector<double> getScalarData()
+    {
+        return {100, 101, 102, 103, 104, 105, 106, 107, 108, 109};
+    }
+
+    static std::vector<double> getKVDataDefaultOrder()
+    {
+        if constexpr (dim == 2)
+        {
+            return {0, 10, 20, 30, 40, 50, 60, 70, 80, 90,   // 1st comp
+                    1, 11, 21, 31, 41, 51, 61, 71, 81, 91,   // 2nd comp
+                    2, 12, 22, 32, 42, 52, 62, 72, 82, 92,   // 3rd comp
+                    3, 13, 23, 33, 43, 53, 63, 73, 83, 93};  // 4th comp
+        }
+        else if constexpr (dim == 3)
+        {
+            return {0, 10, 20, 30, 40, 50, 60, 70, 80, 90,  //
+                    1, 11, 21, 31, 41, 51, 61, 71, 81, 91,  //
+                    2, 12, 22, 32, 42, 52, 62, 72, 82, 92,  //
+                    3, 13, 23, 33, 43, 53, 63, 73, 83, 93,  //
+                    4, 14, 24, 34, 44, 54, 64, 74, 84, 94,  //
+                    5, 15, 25, 35, 45, 55, 65, 75, 85, 95};
+        };
+    }
+
+    static std::vector<double> getKVDataTransposedOrder()
+    {
+        if constexpr (dim == 2)
+        {
+            return {0,  1,  2,  3,   // 1st IP
+                    10, 11, 12, 13,  // 2nd IP
+                    20, 21, 22, 23,  // 3rd IP
+                    30, 31, 32, 33,  // ...
+                    40, 41, 42, 43,  //
+                    50, 51, 52, 53,  //
+                    60, 61, 62, 63,  //
+                    70, 71, 72, 73,  //
+                    80, 81, 82, 83,  //
+                    90, 91, 92, 93};
+        }
+        else if constexpr (dim == 3)
+        {
+            return {
+                0,  1,  2,  3,  4,  5,   //
+                10, 11, 12, 13, 14, 15,  //
+                20, 21, 22, 23, 24, 25,  //
+                30, 31, 32, 33, 34, 35,  //
+                40, 41, 42, 43, 44, 45,  //
+                50, 51, 52, 53, 54, 55,  //
+                60, 61, 62, 63, 64, 65,  //
+                70, 71, 72, 73, 74, 75,  //
+                80, 81, 82, 83, 84, 85,  //
+                90, 91, 92, 93, 94, 95,
+            };
+        };
+    }
+};
+
+using ProcessLib_IPDataAccess_TestCases =
+    ::testing::Types<std::integral_constant<int, 2>,
+                     std::integral_constant<int, 3>>;
+
+TYPED_TEST_SUITE(ProcessLib_IPDataAccess, ProcessLib_IPDataAccess_TestCases);
+
+TYPED_TEST(ProcessLib_IPDataAccess, GetScalarData)
+{
+    constexpr int dim = TypeParam::value;
+
+    auto const ip_data = this->getIPData();
+
+    std::vector<double> cache;
+
+    ProcessLib::getIntegrationPointScalarData(
+        ip_data, &IPData<dim>::scalar, cache);
+
+    ASSERT_THAT(cache,
+                testing::Pointwise(testing::DoubleEq(), this->getScalarData()));
+}
+
+TYPED_TEST(ProcessLib_IPDataAccess, GetKelvinVectorDataDefaultOrder)
+{
+    constexpr int dim = TypeParam::value;
+
+    auto const ip_data = this->getIPData();
+
+    std::vector<double> cache;
+
+    ProcessLib::getIntegrationPointKelvinVectorData<dim>(
+        ip_data, &IPData<dim>::kelvin, cache);
+
+    ASSERT_THAT(
+        cache,
+        testing::Pointwise(testing::DoubleEq(), this->getKVDataDefaultOrder()));
+}
+
+TYPED_TEST(ProcessLib_IPDataAccess, GetKelvinVectorDataTransposedOrder)
+{
+    constexpr int dim = TypeParam::value;
+
+    auto const ip_data = this->getIPData();
+
+    const std::vector<double> cache =
+        ProcessLib::getIntegrationPointKelvinVectorData<dim>(
+            ip_data,
+            &IPData<dim>::kelvin);  // pretty subtle: if no cache argument is
+                                    // passed, data is returned transposed
+
+    ASSERT_THAT(cache,
+                testing::Pointwise(testing::DoubleEq(),
+                                   this->getKVDataTransposedOrder()));
+}
+
+TYPED_TEST(ProcessLib_IPDataAccess, SetScalarData)
+{
+    constexpr int dim = TypeParam::value;
+
+    auto ip_data = this->getIPDataNaNs();
+
+    auto const cache = this->getScalarData();
+
+    auto const num_read = ProcessLib::setIntegrationPointScalarData(
+        &cache[0], ip_data, &IPData<dim>::scalar);
+
+    ASSERT_EQ(ip_data.size(), num_read);
+
+    auto const ip_data_expected = this->getIPData();
+
+    for (std::size_t i = 0; i < ip_data_expected.size(); ++i)
+    {
+        EXPECT_DOUBLE_EQ(ip_data_expected[i].scalar, ip_data[i].scalar)
+            << "Values at integration point " << i << " differ.";
+    }
+}
+
+TYPED_TEST(ProcessLib_IPDataAccess, SetKelvinVectorData)
+{
+    constexpr int dim = TypeParam::value;
+
+    auto ip_data = this->getIPDataNaNs();
+
+    auto const cache = this->getKVDataTransposedOrder();
+
+    auto const num_read = ProcessLib::setIntegrationPointKelvinVectorData<dim>(
+        &cache[0], ip_data, &IPData<dim>::kelvin);
+
+    ASSERT_EQ(ip_data.size(), num_read);
+
+    auto const ip_data_expected = this->getIPData();
+
+    for (std::size_t i = 0; i < ip_data_expected.size(); ++i)
+    {
+        EXPECT_THAT(
+            ip_data[i].kelvin,
+            testing::Pointwise(testing::DoubleEq(), ip_data_expected[i].kelvin))
+            << "Values at integration point " << i << " differ.";
+    }
+}

scripts/ci/jobs/ci_images.yml

@@ -32,6 +32,7 @@ ci_images:
     - |
       echo "CONTAINER_GCC_IMAGE=${CONTAINER_REGISTRY}/gcc:${CONTAINER_TAG}" >> build.env
       echo "CONTAINER_GCC_GUI_IMAGE=${CONTAINER_REGISTRY}/gcc-gui:${CONTAINER_TAG}" >> build.env
+      echo "CONTAINER_GCC_PM_OFF_IMAGE=${CONTAINER_REGISTRY}/gcc-pm-off:${CONTAINER_TAG}" >> build.env
       echo "CONTAINER_CLANG_IMAGE=${CONTAINER_REGISTRY}/clang:${CONTAINER_TAG}" >> build.env
       echo "XUNIT_TO_JUNIT_IMAGE=${CONTAINER_REGISTRY}/xunit-to-junit:${CONTAINER_TAG}" >> build.env
       echo "PRECOMMIT_IMAGE=${CONTAINER_REGISTRY}/pre-commit:${CONTAINER_TAG}" >> build.env
@@ -55,6 +56,13 @@ ci_images:
       --tag $CONTAINER_GCC_GUI_IMAGE --upload
       --cpu-target $CPU_TARGET
       --packages build-essential
+    - poetry run ogscm compiler.py mpi.py ogs.py --build --ogs off
+      --compiler_version 11
+      --pm off --ccache
+      --version_file ../../web/data/versions.json
+      --tag $CONTAINER_GCC_PM_OFF_IMAGE --upload
+      --cpu-target $CPU_TARGET
+      --packages build-essential jq moreutils
     - poetry run ogscm compiler.py ogs.py --build --ogs off
       --compiler clang --compiler_version 11 --ccache
       --version_file ../../web/data/versions.json

scripts/ci/jobs/package.yml

 create cpm cache:
   stage: package
-  dependencies: [meta]
-  tags: [shell, envinf]
+  tags: [docker]
+  needs: [meta, ci_images]
+  image: $CONTAINER_GCC_PM_OFF_IMAGE
   rules:
     - if: $CI_COMMIT_TITLE == "[versions] Updated cpm cache info."
       when: never
@@ -47,9 +48,11 @@ create cpm cache:
         # Remove merge commit:
         if [ $(git show --no-patch --format="%P" HEAD | wc -w) -eq 2 ]; then git checkout HEAD^2; fi
         git diff
+        git config --global user.name "project_120_bot2"
+        git config --global user.email "project_120_bot2-no-reply@opengeosys.org"
         git add ${_versions_file}
-        git commit -m "[versions] Updated cpm cache info."
-        git push git@${CI_SERVER_HOST}:${CI_MERGE_REQUEST_SOURCE_PROJECT_PATH}.git HEAD:${CI_COMMIT_REF_NAME}
+        git commit -n -m "[versions] Updated cpm cache info."
+        git push "https://project_120_bot2:${REPO_WRITE_KEY}@${CI_SERVER_HOST}/${CI_MERGE_REQUEST_SOURCE_PROJECT_PATH}" HEAD:${CI_COMMIT_REF_NAME}
         exit 255 # marks with warning
       fi
     # external dependencies:
@@ -70,11 +73,11 @@ create cpm cache:
 
 offline configure:
   stage: package
-  needs:
-    - job: meta
-  tags: [shell, envinf]
+  tags: [docker]
+  needs: [meta, ci_images]
+  image: $CONTAINER_GCC_PM_OFF_IMAGE
   rules:
-    - if: $CI_COMMIT_TITLE == "[versions] Updated cpm cache info."
+    # For testing: remove rules-directive
     - if: '$CI_COMMIT_BRANCH == "master"'
   variables:
     BUILD_DIR: "../build/offline"
@@ -91,10 +94,8 @@ offline configure:
       wget --no-verbose --header "JOB-TOKEN: $CI_JOB_TOKEN" \
         ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/generic/external-dependencies/${EXT_VERSION}/ext.tar.gz
     - tar xf ext.tar.gz
-    # Disable network access for CPM CMake run, does not work with petsc.
     - |
-      firejail --noprofile --net=none --blacklist=/usr/bin/mfront --read-write=${CI_BUILDS_DIR} \
-        cmake ../../ogs -B . -G Ninja --preset release \
+      cmake ../../ogs -B . -G Ninja --preset release \
           -DOGS_USE_PYTHON=OFF -DOGS_DOWNLOAD_CPM_CACHE=ON
       rm CMakeCache.txt
       cmake ../../ogs -B . -G Ninja --preset release-petsc \

scripts/cmake/DependenciesExternalProject.cmake

@@ -212,7 +212,9 @@ string(REPLACE "." "_" HDF5_TAG ${ogs.tested_version.hdf5})
 set(_hdf5_source GIT_REPOSITORY https://github.com/HDFGroup/hdf5.git GIT_TAG
                  hdf5-${HDF5_TAG}
 )
-set(_hdf5_source_file ${OGS_EXTERNAL_DEPENDENCIES_CACHE}/hdf5-${HDF5_TAG}.zip)
+set(_hdf5_source_file
+    ${OGS_EXTERNAL_DEPENDENCIES_CACHE}/hdf5-${ogs.tested_version.hdf5}.zip
+)
 if(EXISTS ${_hdf5_source_file})
     set(_hdf5_source URL ${_hdf5_source_file})
 elseif(NOT OGS_BUILD_HDF5)

scripts/cmake/DocumentationSetup.cmake

@@ -90,6 +90,7 @@ if($ENV{CI_COMMIT_BRANCH} MATCHES "master|^v[0-9]\.[0-9]\.[0-9]")
     set(DOXYGEN_SEARCHENGINE_URL
         "https://doxysearch.opengeosys.org/$ENV{CI_COMMIT_BRANCH}/doxysearch.cgi"
     )
+    set(DOXYGEN_SEARCHENGINE YES)
     message(STATUS "Doxygen search server: ${DOXYGEN_SEARCHENGINE_URL}")
 endif()
 if(EXISTS ${PROJECT_BINARY_DIR}/cpp-dependencies.svg)

web/content/docs/devguide/procedures/publish-a-release/index.md

@@ -27,7 +27,7 @@ weight = 1080
 - Check if a [Zenodo release](https://zenodo.org/account/settings/github/repository/ufz/ogs#) is automatically issued
 - Issue a scan on [Software Heritage Archive](https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://gitlab.opengeosys.org/ogs/ogs.git)
 - Update `CITATION.cff` and `web/content/publications/_index.md` with new Zenodo DOI
-- Update `CITATION.cff` author list (`git shortlog -sne`) and corresponding bibtex-entry in publications web page
+- Update `CITATION.cff` author list (`git shortlog -sne 6.4.3...6.4.2`) and corresponding bibtex-entry in publications web page
 - Create bugfix branch
   - Create new netlify site (in an empty directory)
     <!-- vale off -->

web/content/publications/_index.md

@@ -12,22 +12,36 @@ weight = 3
 ### Cite the software
 
 ```bibtex
-@software{ogs:6.4.2,
-  author = {Naumov, Dmitry Yu. and Bilke, Lars and Fischer, Thomas and
-            Rink, Karsten and Wang, Wenqing and Watanabe, Norihiro and
-            Lu, Renchao and Grunwald, Norbert and Zill, Florian and
-            Buchwald, Jörg and Huang, Yonghui and Bathmann, Jasper and
-            Chen, Chaofan and Chen, Shuang and Meng, Boyan and
-            Shao, Haibing and Kern, Dominik and Yoshioka, Keita and
-            Garibay Rodriguez, Jaime and Miao, Xingyuan and
-            Parisio, Francesco and Silbermann, Christian and Thiedau, Jan and
-            Walther, Marc and Kaiser, Sonja and Boog, Johannes and
-            Zheng, Tianyuan and Meisel, Tobias and Ning, Zhang},
-  doi    = {10.5281/zenodo.6405711},
-  month  = {4},
-  title  = {OpenGeoSys},
-  url    = {https://www.opengeosys.org},
-  year   = {2022}
+@software{ogs:6.4.3,
+  author       = {Lars Bilke and
+                  Thomas Fischer and
+                  Dmitri Naumov and
+                  Christoph Lehmann and
+                  Wenqing Wang and
+                  Renchao Lu and
+                  Boyan Meng and
+                  Karsten Rink and
+                  Norbert Grunwald and
+                  Jörg Buchwald and
+                  Christian Silbermann and
+                  Robert Habel and
+                  Linda Günther and
+                  Mostafa Mollaali and
+                  Tobias Meisel and
+                  Jakob Randow and
+                  Sophia Einspänner and
+                  Haibing Shao and
+                  Kata Kurgyis and
+                  Olaf Kolditz and
+                  Jaime Garibay},
+  title        = {OpenGeoSys},
+  month        = apr,
+  year         = 2022,
+  note         = {{If you use this software, please cite it using these metadata.}},
+  publisher    = {Zenodo},
+  version      = {6.4.3},
+  doi          = {10.5281/zenodo.7092676},
+  url          = {https://doi.org/10.5281/zenodo.7092676}
 }
 ```
 

web/data/versions.json

@@ -71,8 +71,8 @@
     }
   },
   "cpm": {
-    "package_file_id": 182,
-    "package_file_sha256": "00d7dea24754ad415e7003535b36a7d5b4e7224701341f5ca587f93e42b63563"
+    "package_file_id": 193,
+    "package_file_sha256": "999f770315795d9de91b6a97e5e1cdee9c0256cd338977ff9a5ec9ff79b7fd0e"
   },
   "ext": {
     "cache_hash": "e6f3f1f4c29c6c5f096f89785e6e245bdf39ac1a"